Distinguishing Noise from Signal in Patterns of Genomic Divergence in a Highly Polymorphic Avian Radiation

Campagna, L., Gronau, I., Silveira, L. F., Siepel, A., Lovette, I. J. (2015) Distinguishing Noise from Signal in Patterns of Genomic Divergence in a Highly Polymorphic Avian Radiation. Mol Ecol, 24 (16). pp. 4238-4251. ISSN 1365-294X (Electronic)0962-1083 (Linking)

URL: http://www.ncbi.nlm.nih.gov/pubmed/26175196
DOI: 10.1111/mec.13314

Abstract

Recently diverged taxa provide the opportunity to search for the genetic basis of the phenotypes that distinguish them. Genomic scans aim to identify loci that are diverged with respect to an otherwise weakly differentiated genetic background. These loci are candidates for being past targets of selection because they behave differently from the rest of the genome that has either not yet differentiated, or that may cross species barriers through introgressive hybridization. Here we use a reduced representation genomic approach to explore divergence among six species of southern capuchino seedeaters, a group of recently radiated sympatric passerine birds in the genus Sporophila. For the first time in these taxa, we discovered a small proportion of markers that appeared differentiated among species. However, when assessing the significance of these signatures of divergence, we found that similar patterns can also be recovered from random grouping of individuals representing different species. A detailed demographic inference indicates that genetic differences among Sporophila species could be the consequence of neutral processes, which include a very large ancestral effective population size that accentuates the effects of incomplete lineage sorting. As these neutral phenomena can generate genomic scan patterns that mimic those of markers involved in speciation and phenotypic differentiation, they highlight the need for caution when ascertaining and interpreting differentiated markers between species, especially when large numbers of markers are surveyed. Our study provides new insights into the demography of the southern capuchino radiation and proposes controls to distinguish signal from noise in similar genomic scans. This article is protected by copyright. All rights reserved.

Item Type: Paper
Uncontrolled Keywords: Drift Genomic Scan Incomplete Lineage Sorting Outlier Analysis RAD sequencing Species Flock
Subjects: bioinformatics
bioinformatics > genomics and proteomics
organism description > animal > bird
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
CSHL Authors:
Communities: CSHL labs > Siepel lab
Depositing User: Matt Covey
Date Deposited: 16 Jul 2015 19:01
Last Modified: 31 Aug 2015 19:41
Related URLs:
URI: http://repository.cshl.edu/id/eprint/31630

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